Examples with MemVariable cbit.vcell.math.MemVariable used on opensource projects

Example 11 with MemVariable

use of cbit.vcell.math.MemVariable in project vcell by virtualcell.

the class MathOverridesPanel method jMenuItemPaste_ActionPerformed.

/**
 * Comment
 */
private void jMenuItemPaste_ActionPerformed(java.awt.event.ActionEvent actionEvent) {
    java.util.Vector<String> pasteDescriptionsV = new java.util.Vector<String>();
    java.util.Vector<Expression> newConstantsV = new java.util.Vector<Expression>();
    java.util.Vector<String> changedParameterNamesV = new java.util.Vector<String>();
    try {
        if (actionEvent.getSource().equals(getJMenuItemPaste()) || actionEvent.getSource().equals(getJMenuItemPasteAll())) {
            int[] rows = null;
            if (actionEvent.getSource() == getJMenuItemPasteAll()) {
                rows = new int[getJTableFixed().getRowCount()];
                for (int i = 0; i < rows.length; i += 1) {
                    rows[i] = i;
                }
            } else {
                rows = getJTableFixed().getSelectedRows();
            }
            Object pasteThis = VCellTransferable.getFromClipboard(VCellTransferable.OBJECT_FLAVOR);
            for (int i = 0; i < rows.length; i += 1) {
                if (pasteThis instanceof VCellTransferable.ResolvedValuesSelection) {
                    VCellTransferable.ResolvedValuesSelection rvs = (VCellTransferable.ResolvedValuesSelection) pasteThis;
                    for (int j = 0; j < rvs.getPrimarySymbolTableEntries().length; j += 1) {
                        Constant pastedConstant = null;
                        if (rvs.getPrimarySymbolTableEntries()[j] instanceof Constant) {
                            pastedConstant = (Constant) rvs.getPrimarySymbolTableEntries()[j];
                        } else if (rvs.getAlternateSymbolTableEntries() != null && rvs.getAlternateSymbolTableEntries()[j] instanceof Constant) {
                            pastedConstant = (Constant) rvs.getAlternateSymbolTableEntries()[j];
                        }
                        // 
                        if (pastedConstant == null && (rvs.getPrimarySymbolTableEntries()[j] instanceof Function) || (rvs.getPrimarySymbolTableEntries()[j] instanceof VolVariable) || (rvs.getPrimarySymbolTableEntries()[j] instanceof VolumeRegionVariable) || (rvs.getPrimarySymbolTableEntries()[j] instanceof MemVariable) || (rvs.getPrimarySymbolTableEntries()[j] instanceof MembraneRegionVariable)) {
                            MathDescription mathDescription = getMathOverrides().getSimulation().getMathDescription();
                            Enumeration<Constant> constants = mathDescription.getConstants();
                            while (constants.hasMoreElements()) {
                                Constant constant = constants.nextElement();
                                if (constant.getName().startsWith(rvs.getPrimarySymbolTableEntries()[j].getName() + DiffEquMathMapping.MATH_FUNC_SUFFIX_SPECIES_INIT_CONC_UNIT_PREFIX)) {
                                    pastedConstant = new Constant(constant.getName(), rvs.getExpressionValues()[j]);
                                }
                            }
                        }
                        // 
                        // find row of math overrides table with the same name as the pastedConstant and propose to change that override to the pasted value
                        // 
                        String rowName = (String) getJTableFixed().getValueAt(rows[i], MathOverridesTableModel.COLUMN_PARAMETER);
                        if (pastedConstant != null && pastedConstant.getName().equals(rowName)) {
                            changedParameterNamesV.add(rowName);
                            newConstantsV.add(rvs.getExpressionValues()[j]);
                            String originalValueDescription = null;
                            if (getMathOverrides().getConstantArraySpec(rowName) != null) {
                                originalValueDescription = getMathOverrides().getConstantArraySpec(rowName).toString();
                            } else if (getMathOverrides().getActualExpression(rowName, 0) != null) {
                                originalValueDescription = getMathOverrides().getActualExpression(rowName, 0).infix();
                            } else {
                                throw new Exception("MathOverridesPanel can't find value for '" + rowName + "'");
                            }
                            pasteDescriptionsV.add(VCellCopyPasteHelper.formatPasteList(rowName, pastedConstant.getName(), originalValueDescription, rvs.getExpressionValues()[j].infix() + ""));
                        }
                    }
                }
            }
        }
    } catch (Throwable e) {
        PopupGenerator.showErrorDialog(this, "Paste failed during pre-check (no changes made).\n" + e.getClass().getName() + " " + e.getMessage(), e);
        return;
    }
    // Do paste
    try {
        if (pasteDescriptionsV.size() > 0) {
            String[] pasteDescriptionArr = new String[pasteDescriptionsV.size()];
            pasteDescriptionsV.copyInto(pasteDescriptionArr);
            String[] changedParameterNamesArr = new String[changedParameterNamesV.size()];
            changedParameterNamesV.copyInto(changedParameterNamesArr);
            VCellCopyPasteHelper.chooseApplyPaste(this, pasteDescriptionArr, getMathOverrides(), changedParameterNamesArr, newConstantsV);
        } else {
            PopupGenerator.showInfoDialog(this, "No paste items match the destination (no changes made).");
        }
    } catch (Throwable e) {
        PopupGenerator.showErrorDialog(this, "Paste Error\n" + e.getClass().getName() + " " + e.getMessage(), e);
    }
}

Example 12 with MemVariable

use of cbit.vcell.math.MemVariable in project vcell by virtualcell.

the class FastSystemAnalyzer method refreshFastVarList.

/**
 * @return java.util.Vector
 */
private void refreshFastVarList() throws MathException, ExpressionException {
    fastVarList.clear();
    // 
    // get list of unique (VolVariables and MemVariables) in fastRate expressions
    // 
    Enumeration<FastRate> fastRatesEnum = fastSystem.getFastRates();
    while (fastRatesEnum.hasMoreElements()) {
        FastRate fr = fastRatesEnum.nextElement();
        Expression exp = fr.getFunction();
        Enumeration<Variable> enum1 = MathUtilities.getRequiredVariables(exp, this);
        while (enum1.hasMoreElements()) {
            Variable var = enum1.nextElement();
            if (var instanceof VolVariable || var instanceof MemVariable) {
                if (!fastVarList.contains(var)) {
                    fastVarList.addElement(var);
                // System.out.println("FastSystemImplicit.refreshFastVarList(), FAST RATE VARIABLE: "+var.getName());
                }
            }
        }
    }
    // 
    // get list of all variables used in invariant expressions that are not used in fast rates
    // 
    Enumeration<FastInvariant> fastInvariantsEnum = fastSystem.getFastInvariants();
    while (fastInvariantsEnum.hasMoreElements()) {
        FastInvariant fi = (FastInvariant) fastInvariantsEnum.nextElement();
        Expression exp = fi.getFunction();
        // System.out.println("FastSystemImplicit.refreshFastVarList(), ORIGINAL FAST INVARIANT: "+exp);
        Enumeration<Variable> enum1 = MathUtilities.getRequiredVariables(exp, this);
        while (enum1.hasMoreElements()) {
            Variable var = enum1.nextElement();
            if (var instanceof VolVariable || var instanceof MemVariable) {
                if (!fastVarList.contains(var)) {
                    fastVarList.addElement(var);
                }
            }
        }
    }
    // 
    // verify that there are N equations (rates+invariants) and N unknowns (fastVariables)
    // 
    int numBoundFunctions = fastSystem.getNumFastInvariants() + fastSystem.getNumFastRates();
    if (fastVarList.size() != numBoundFunctions) {
        throw new MathException("FastSystem.checkDimension(), there are " + fastVarList.size() + " variables and " + numBoundFunctions + " FastInvariant's & FastRates");
    }
}

Example 13 with MemVariable

use of cbit.vcell.math.MemVariable in project vcell by virtualcell.

the class MathMapping_4_8 method refreshVariables.

/**
 * This method was created in VisualAge.
 */
private void refreshVariables() throws MappingException {
    // System.out.println("MathMapping.refreshVariables()");
    // 
    // non-constant dependent variables require a function
    // 
    Enumeration<SpeciesContextMapping> enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = enum1.nextElement();
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        if (scm.getDependencyExpression() != null && !scs.isConstant()) {
            // scm.setVariable(new Function(scm.getSpeciesContext().getName(),scm.getDependencyExpression()));
            scm.setVariable(null);
        }
    }
    enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = enum1.nextElement();
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        if (getSimulationContext().hasEventAssignment(scs.getSpeciesContext())) {
            scm.setDependencyExpression(null);
        }
    }
    // 
    // non-constant independent variables require either a membrane or volume variable
    // 
    enum1 = getSpeciesContextMappings();
    while (enum1.hasMoreElements()) {
        SpeciesContextMapping scm = (SpeciesContextMapping) enum1.nextElement();
        SpeciesContextSpec scs = simContext.getReactionContext().getSpeciesContextSpec(scm.getSpeciesContext());
        if (scm.getDependencyExpression() == null && (!scs.isConstant() || getSimulationContext().hasEventAssignment(scs.getSpeciesContext()))) {
            StructureMapping sm = simContext.getGeometryContext().getStructureMapping(scm.getSpeciesContext().getStructure());
            Structure struct = scm.getSpeciesContext().getStructure();
            if (struct instanceof Feature) {
                if (getResolved(sm)) {
                    scm.setVariable(getResolvedVolVariable(scm.getSpeciesContext().getSpecies()));
                } else {
                    scm.setVariable(new VolVariable(scm.getSpeciesContext().getName(), nullDomain));
                }
            } else if (struct instanceof Membrane) {
                if (getResolved(sm)) {
                    scm.setVariable(new MemVariable(scm.getSpeciesContext().getName(), nullDomain));
                } else {
                    scm.setVariable(new VolVariable(scm.getSpeciesContext().getName(), nullDomain));
                }
            } else {
                throw new MappingException("class " + scm.getSpeciesContext().getStructure().getClass() + " not supported");
            }
            mathSymbolMapping.put(scm.getSpeciesContext(), scm.getVariable().getName());
        }
    }
}

Example 14 with MemVariable

use of cbit.vcell.math.MemVariable in project vcell by virtualcell.

the class XmlReader method getMemVariable.

/**
 * This method returns a MemVariable object from a XML element.
 * Creation date: (5/16/2001 3:17:18 PM)
 * @return cbit.vcell.math.MemVariable
 * @param param org.jdom.Element
 */
private MemVariable getMemVariable(Element param) {
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    String domainStr = unMangle(param.getAttributeValue(XMLTags.DomainAttrTag));
    Domain domain = null;
    if (domainStr != null) {
        domain = new Domain(domainStr);
    }
    // Create new memVariable
    MemVariable memVariable = new MemVariable(name, domain);
    transcribeComments(param, memVariable);
    return memVariable;
}

Example 15 with MemVariable

use of cbit.vcell.math.MemVariable in project vcell by virtualcell.

the class XmlReader method getComputeNormal.

private ComputeNormalComponentEquation getComputeNormal(Element param, MathDescription mathDesc) throws XmlParseException {
    // get attributes
    String varname = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    // find reference in the dictionnary
    // try a MembraneRegionVariable
    MemVariable varref = (MemVariable) mathDesc.getVariable(varname);
    if (varref == null) {
        throw new XmlParseException("The reference to the Membrane variable " + varname + " could not be resolved!");
    }
    NormalComponent normalComponent = null;
    String normalComponentString = param.getAttributeValue(XMLTags.ComputeNormalComponentAttrTag);
    if (normalComponentString.equals(XMLTags.ComputeNormalComponentAttrTagValue_X)) {
        normalComponent = NormalComponent.X;
    } else if (normalComponentString.equals(XMLTags.ComputeNormalComponentAttrTagValue_Y)) {
        normalComponent = NormalComponent.Y;
    } else if (normalComponentString.equals(XMLTags.ComputeNormalComponentAttrTagValue_Z)) {
        normalComponent = NormalComponent.Z;
    }
    ComputeNormalComponentEquation computeNormal = new ComputeNormalComponentEquation(varref, normalComponent);
    return computeNormal;
}